Mobs which are intended to be persistant will occasionally vanish from the game.

I have created a village in which there are trapped persistant mobs; villagers, tame cats, and tame dogs. Periodically, if the chunk containing said mobs is unloaded and then reloaded, one or more of them will be gone. I have performed tests and ensured they could not have escaped or have been killed (fully enclosed, peaceful mode). This happens in both single player and multiplayer. I suspect they may be falling though the floors, but have been unable to verify it because if the mob is loading before the chunk, it would fall into the void. It is tricky to duplicate, as it seems to happen at random. All of the mobs may remain through many chunk unloads and loads before one will suddenly disappear.